Does the same bonus (e.g. noise reduction) via skill tree (40%) and via clothing (40%) stack to give 80% noise reduction?
If yes, perhaps charactor profile should show all active bonuses along with clothing bonus.
If not, somewhere it should be stated that skill and clothing bonuses do not stack.
Would be much obliged if this has already been clarified before and point me to that source.
I think bonuses from different sources stack - but don’t know if it’s been explicitly stated anywhere. 
Yes, I think they should stack.
And, I agree. We already have debuff icons for various types of damage, so having positive buff icons for active bonuses makes sense 
Are you sure? I have the Vanguard specialization unlocked and almost a full set of clothes unlocked with ballistic protection which should give me, 75% bullet resistance yet a single barrage of bullets from one of the hunters will leave me with near no health.
There was an issue where bullet resistance was bugged, idk if it was fixed but if you can actually supply evidence of it not working it would be very much worth to do a bug report.
E.g. use no bullet resistance clothing, get hit by a Tank railgun, screenshot health, and then do the same with the full clothing, take screenshot, then do the same with clothing + perks, screenshot.
I might actually try this myself.
tenebris utube channel talked about clothing stacks, he tested them with invisiblelity & noise, don’t go over 50% , or it will go into negative